tbuckley/cabot-search huggingface dataset:
Abstract 3451: Interpreting gene lists from -omics experiments
Authors: Augustin Luna, Jeffrey V. Wong, Emek Demir, Igor Rodchenkov, Özgün Babur, Chris Sander, Gary D. Bader
Journal: Cancer Research (2019)

Abstract Understanding the mechanisms responsible for a cellular behavior often begins with observations of genes and gene products. Depending on the type of experiment, the number of resulting genes can be small, but increasingly, researchers are faced with many thousands of measurements, as in the case of transcriptomic or protein-DNA binding observations. Here, we describe ways to pair experimental results consisting of one or more genes with analysis tools with the overall aim being to make results more biologically interpretable. In certain cases, experimental approaches such as screens for essential genes can generate one or a few ‘genes of interest’ and there is a desire to understand their relationship to one another as well as discover links to additional, interesting genes. To this end, ‘GeneMANIA’ is a web tool that accepts gene names and returns a network visualization of related genes based on similarity in expression, localization, protein domains and those involved in physical interactions. Likewise, ‘PCViz’ is a web tool that displays a network of interactions drawn from Pathway Commons, a web resource for pathway and interaction knowledge. In cases where experiments generate a lengthy list of genes, for instance, transcriptomic measurements, there is a desire to understand their relevance to a phenotype of interest. Pathway enrichment analysis methods aim to summarize gene lists as pathways, which have a closer link to cell function. An online ‘Guide’ by Pathway Commons includes workflows that illustrate how to chain together software tools to identify pathways from the corresponding gene-level data then organize and summarize the pathway-level results in an interactive visualization known as an Enrichment Map. For those wishing to drill-down to individual pathways, Pathway Commons offers a set of web apps, including ‘Search’ that enables users to query by keyword and visualize ranked search results. Ongoing development of web apps aims to enhance the accessibility to pathways and integrate support for analysis and visualization of experimental data. The full complement of data, tools and resources offered by Pathway Commons in support of pathway analysis are described. Citation Format: Augustin Luna, Jeffrey V. Wong, Emek Demir, Igor Rodchenkov, Özgün Babur, Chris Sander, Gary D. Bader. Interpreting gene lists from -omics experiments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3451.
Changes in levels of catalase and glutathione in erythrocytes of patients with stable asthma, treated with beclomethasone dipropionate
Authors: H.J. Pennings, P.J.A. Borm, C.T.a Evelo, E.F.m Wouters
Journal: European Respiratory Journal (1999)

Cross-sectional studies have suggested that asthmatic patients receiving high dose inhaled corticosteroids and intermittent courses of oral corticosteroids have reduced bone mass. This prospective 2-yr study was undertaken to evaluate changes in bone density of patients receiving high doses of inhaled corticosteroids. Patients (n = 33) (males aged 18-50 yrs, females aged 18-40 yrs) on inhaled corticosteroids 1,000-2,000 microg x day(-1), were randomized in a double-blind fashion to either fluticasone propionate (FP) 1,000 microg x day(-1) or beclomethasone dipropionate (BDP) 2,000 microg x day(-1). In parallel, three open control groups of the same age range were studied: asthmatics (n = 8) receiving low dose inhaled corticosteroids (&lt; or =400 microg x day(-1)) (group A); chronic, severe asthmatics (n = 8) receiving oral corticosteroids (&gt; or =10 mg x day(-1) (group B); and healthy untreated volunteers (n = 7) (group C). Bone densitometry scans (quantitative computed tomography (QCT) of spine; dual X-ray absorptiometry of spine, femoral neck, and single photon absorptiometry of forearm) were performed at baseline and after 6, 12 and 24 months of treatment. Biochemical bone marker measurements (serum osteocalcin, bone alkaline phosphatase, pro-collagen type 1 carboxy terminal propeptide, deoxypyridinoline and C-telopeptide of type 1 collagen) were collected every 3 months. Fifteen FP (mean age 36 yrs, six male) and 9 BDP patients (mean age 33 yrs, five male); completed the study. At 0 months, mean bone mineral density (BMD) was lower in patients receiving inhaled corticosteroids (both low dose and high dose) than in normal volunteers. In the FP-treated group, mean vertebral trabecular BMD quantitative computed tomography remained stable with no evidence of decline, whereas there was some decline in the BDP-treated group. The treatment difference between FP and BDP was statistically significant in favour of FP for quantitative computed tomography measurements after 12 months (p = 0.006) and 24 months (p = 0.004). This study suggests that over 24 months, changes in bone density are minimal in patients on high-dose inhaled corticosteroids.
Medical Education and State Boards of Registration.
Journal: JAMA (1906)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Pathological Basis of Multiple Sclerosis
Journal: JAMA (1963)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
A treasured treasurer
Authors: R. Smith
Journal: BMJ (1996)

The question of causation remains open.The provocative "oestrogen hypothesis""9 remains a hypothesis, albeit one which is gathering biological weight,'2 2 and clinical data are scarce.Taken together, the available data on semen quality and other aspects of male reproductive health, at the very least, raise concerns that should be addressed by properly designed, coordinated, and funded research.Prospective multicentre studies with attention to possible confounding factors and appropriate quality control are required, together with more reliable methods of assessing semen quality.To paraphrase a recent BMY editorial,= delay may compromise the reproduc- tive health of future generations.
Brain Abscess
Authors: Marco Rizzi, Diego Ripamonti
Journal: New England Journal of Medicine (2014)

placebo group received subsequent life-extending therapy at the time of data cutoff.At that time, of the 251 patients in the placebo group who had not received subsequent life-extending therapy, 24% continued to receive placebo, 19% received other therapies, and 43% died before receiving any subsequent therapy.We would suggest that the timing of chemotherapy in such patients has not been shown to affect survival and that the post-progression treatment experience of our study patients reflects the standard of care.
Correction
Journal: BMJ (1955)

MIC&B.,nJOURNkL greatly diminish or arrest ciliary movement.This move- ment normally removes the tarry deposits from tobacco smoke which are formed in the bronchioles.The tar is transported from the respiratory passages into the oeso- phagus.The cough probably arises from the irritation caused by the tarry deposits, and would be made worse if the removal of these deposits were impeded.
Abstract P030: Variations in Cardiovascular Risk Among Different Clinical Presentations of Metabolic Syndrome in the REasons for Geographic And Racial Differences in Stroke (REGARDS) Study
Authors: Todd M Brown, Joshua Richman, Vera Bittner, Cora E Lewis, Jenifer Voeks, Monika M Safford
Journal: Circulation (2012)

Background: Some individuals classified as having metabolic syndrome (MetSyn) are centrally obese while others are not with unclear implications for cardiovascular (CV) risk. Methods: REGARDS is following 30,239 individuals ≥45 years of age living in 48 states recruited from 2003-7. MetSyn risk factors were defined using the AHA/NHLBI/IDF harmonized criteria with central obesity being defined as ≥88 cm in women and ≥102 cm in men. Participants with and without central obesity were stratified by whether they met &gt;2 or ≤2 of the other 4 MetSyn criteria, resulting in the creation of 4 groups. To ascertain CV events, participants are telephoned every 6 months with expert adjudication of potential events following national consensus recommendations and based on medical records, death certificates, and interviews with next-of-kin or proxies. Acute coronary heart disease (CHD) was defined as definite or probable myocardial infarction or acute CHD death. To determine the association between these 4 groups and incident acute CHD, we constructed Cox proportional hazards models in those free of CHD at baseline by race/gender group, adjusting for sociodemographic variables. Results: A total of 20,018 individuals with complete data on MetSyn components were free of baseline CHD. Mean age was 64+/−9 years, 58% were women, and 42% were African American. Over a mean follow-up of 3.4 (maximum 5.9) years, there were 442 acute CHD events. In the non-centrally obese with&gt;2 other risk factors, risk for CHD was higher for all but AA men, though significant only for white men. In contrast, in the centrally obese with &gt;2 other risk factors, risk was doubled for women, but only non-significantly and modestly increased for men. Only AA women with central obesity and ≤2 other risk factors had increased CHD risk (Table). Conclusion: The CHD risk associated with the MetSyn varies by the presence of central obesity as well as the race and gender of the individual.
Editorial Board
Authors: Sian Lewis, Patrick Wilken, Katja Brose, Lewis Packwood, Lara Crow, Mat Mccutcheon, Philip Patenall, Neill Sharp, Anders Björklund, Sweden Lund, Sarah Paul Bolam, Barry Dickson, John Disterhoft, Chris Doe, John Flanagan, Craig Garner, Yukiko Goda, Meyer London, Robert Malenka, Mark Stanford, Richard Mattson, Venkatesh Morris, Maiken Murthy, Nancy Rothwell, Mike Shadlen, Marc Tessier-Lavigne, Chris Walsh, Norman Saunders, C Ek, Mark Habgood, Katarzyna Dziegielewska, Karel Talavera, Bernd Nilius, Thomas Voets, Erik Zornik, Ayako Yamaguchi, W Caudle, Rebecca Colebrooke, Piers Emson, Gary Miller, Daniel Johnston, Rishikesh Narayanan, Takumi Takizawa, Eran Meshorer, J Lawrence, John Fondon, Elizabeth Hammock, Anthony Hannan, David King, Gary Bargary, Kevin Mitchell, Hermann Ackermann, Susan Masino, Jonathan Geiger
Journal: Trends in Neurosciences (2008)
Early Weaning and Hospitalization With Alcohol-Related Diagnoses in Adult Life
Authors: Holger J Sørensen, Erik L Mortensen, June M Reinisch, Sarnoff A Mednick
Journal: American Journal of Psychiatry (2006)

This study attempted to determine whether lack of breast-feeding or a short duration of breast-feeding during infancy is associated with an elevated risk of hospitalization with alcohol-related diagnoses in adult life.The study was a prospective longitudinal birth cohort design conducted in a sample of 6,562 men and women, all of whom were born in Copenhagen, Denmark, between October 1959 and December 1961. The sample was divided into two categories based on duration of breast-feeding, as assessed by a physician interview with mothers at a 1-year examination. Psychiatric hospitalizations with alcohol-related diagnoses according to ICD-8 or ICD-10 were identified in the Danish Psychiatric Central Register in 1999. Nine potential confounders were included as covariates: gender of the cohort member, maternal age, parental social status, maternal prenatal smoking, unwanted pregnancy, maternal and paternal psychiatric hospitalization with alcohol-related diagnosis, and maternal and paternal psychiatric hospitalization with other diagnosis.Alcohol-related diagnoses were more frequent in men, but the results were comparable for men and women. The adjusted predictive effect of early weaning was 1.47. Elevated relative risks were also associated with maternal smoking during pregnancy (1.52) and unwanted pregnancy status (1.59). Other independent predictors were male gender, maternal psychiatric hospitalization with alcohol-related diagnosis, and low parental social status.Independent of a number of other risk factors for alcoholism, a significant association between early weaning and elevated risk of hospitalization with alcohol-related diagnoses was observed.
Abstract 872: Genetic models reveal that the novel <i>VGLL2-NCOA2</i> fusion oncogene leverages embryonic programs for sarcomagenesis
Authors: Genevieve C. Kendall, Sarah Watson, Lin Xu, Collette LaVigne, Whitney Murchison, Dinesh Rakheja, Franck Tirode, Olivier Delattre, James Amatruda
Journal: Cancer Research (2019)

Abstract Rhabdomyosarcoma (RMS) is an aggressive pediatric cancer characterized by a misregulation of skeletal muscle developmental pathways. To date, identified oncogenic drivers predominantly include RAS mutations or chromosomal translocations and gene fusions between PAX3 or PAX7 and FOXO1. RNAseq analysis of sarcomas with non-canonical gene fusions has identified new potential genetic drivers of tumorigenesis that have not been rigorously functionally validated for their transformation capacity and biological activity. One new fusion is a chromosomal translocation and inversion between chromosomes 6 and 8, which acts to juxtapose two transcriptional co-activators, VGLL2 and NCOA2. This VGLL2-NCOA2 fusion was identified in congenital rhabdomyosarcoma clinical cohorts by us and others, and characterizes aggressive RMS that express MYOD and MYOG histological markers. However, evidence of VGLL2-NCOA2 transformation capacity has not been verified, hindering insights into its functional contributions to tumorigenesis. Here, we interrogate the function ofVGLL2-NCOA2 using complementary genomic patient data and zebrafish model systems. We utilized the Tol2 transposon system to express mosaic human VGLL2-NCOA2 during early development, and found that VGLL2-NCOA2 is sufficient for tumorigenesis, and results in aggressive tumors with high penetrance by 75 days of age in zebrafish. Further, the histology of zebrafish tumors resembles the human disease, and tumors express markers indicative of RMS such as myog and desma. A cross-species RNAseq of patient and zebrafish VGLL2-NCOA2 RMS tumors highlights a significant enrichment and overlap between gene expression signatures. Finally, mapping the gene expression signatures of VGLL2-NCOA2 zebrafish RMS tumors along the spectrum of zebrafish embryogenesis indicates a clustering with developmental stages corresponding to early somitogenesis, highlighting their arrested developmental nature. Hence, we have generated the first animal model of human VGLL2-NCOA2 tumorigenesis, and have applied this model to understand the biology and identify potential therapeutic targets for this newly identified disease. Citation Format: Genevieve C. Kendall, Sarah Watson, Lin Xu, Collette LaVigne, Whitney Murchison, Dinesh Rakheja, Franck Tirode, Olivier Delattre, James Amatruda. Genetic models reveal that the novel VGLL2-NCOA2 fusion oncogene leverages embryonic programs for sarcomagenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 872.
Programs of Government Agencies Pertinent to Medical Education
Journal: JAMA (1966)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Stress-Reply
Authors: Norman Cousins
Journal: JAMA (1980)

<h3>In Reply.—</h3> Dr Scherlis seeks to redefine stress in a way that differentiates it from strain. There may be good reasons behind such a redefinition, but I doubt that it will be possible, in the popular or professional mind, to rewrite the language and to detach stress from any suggestion of negative stimulus. All the general dictionaries connect stress to disturbance.<i>Stedman's Medical Dictionary</i>describes stress as "the reactions of the animal body to forces of a deleterious nature [such as] infections and various abnormal states that tend to disturb its normal physiologic equilibrium (homeostasis)." The<i>Encyclopedia Britannica</i>defines stress as "any strain or interference that disturbs the functioning of an organism." Hans Selye, in his<i>Stress of Life</i>,<sup>1</sup>sees it as "the rate of wear and tear in the body." I of course respect the right of any person or any committee to seek acceptance of a new
Marihuana
Authors: Robert G. Faber
Journal: JAMA (1972)

<h3>To the Editor.—</h3> All of the subjects examined were psychiatric patients, which starts out as a rather unreasonably weighted group to choose as the nucleus of an objective study. Many people drink alcohol, after all, but only some become addicted as alcoholics. From the political and social aspects of the stand I have taken regarding official reaction to the use and possession of marihuana, most of the studies that have been conducted generally seem to indicate little adverse effect as the result of the moderate use of marihuana. It is not addictive, nor does it cause the aggressive behavior alcohol does. Furthermore, there is no evidence that the use of marihuana need necessarily lead to the use of LSD or any of the hard drugs. I do not believe the use of marihuana is entirely benign, but I do believe that society's action in trying to control its use is
Serpents, Staffs, and the Emblems of Medicine
Authors: N. W. Williams
Journal: JAMA (1999)

A snake-entwined staff.The oath of Hippocrates.The clinical acumen of Osler and the compassionate service of Schweitzer.These are the symbols and personifications of our chosen profession.One symbol of medicine since antiquity has been the Aesculapian staff. 1 A glance through this journal will uncover the staff in the American Medical Association's emblem, depicting a snake coiled around the rough, knotty staff of the Greek physician Aesculapius.In this issue of MSJAMA, Nathan W. Williams explores the connection between snakes and the art of healing across cultures; Judith Anne Stanton introduces us to Aesculapius.Williams reveals that the serpent can represent the forces of both healing and destruction.Stanton demonstrates that society's alternating praise and distrust of the medical profession have been present throughout time and suggests that such ambivalence will continue.Valerie A. Jones turns her attention to another Greek healer, Hippocrates, who bestowed on modern medicine a legacy of ethical thought embodied in his famous oath.This pledge has become part of a new ceremony that Jones describes in her discussion of a second inherited symbol of the profession-the physician's white coat.Timothy Lahey, MD, argues that we must preserve the purity of the meaning behind such symbols as the white coat by always acting in the best interest of our patients.By exploring the symbols that form and influence the culture of medicine, we hope to come closer to the heart of what it means to be a physician.